Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription
Condensed Matter journal club
Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription
- Event time: 11:30am
- Event date: 30th May 2014
- Speaker: Dr Chris Brackley (School of Physics & Astronomy, University of Edinburgh)
- Location: Room 2511, James Clerk Maxwell Building (JCMB) James Clerk Maxwell Building Peter Guthrie Tait Road Edinburgh EH9 3FD GB
Event details
Abstract
A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model's predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.Cell 157 pages 950-963 (2014)
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Authors
Luca Giorgetti, Rafael Galupa, Elpège P Nora, Tristan Piolot, France Lam, Job Dekker, Guido Tiana, Edith Heard
About Condensed Matter journal club
Given the diversity of research in the CM group, chosen topics vary widely. We tend to stick to high-impact journals - Nature, Science, PNAS and PRL have been popular - but this is not prescriptive..